There's a bug in patching unicode filenames. Are you using any filenames with unicode characters in the file name?
If you are indeed using unicode filenames, this bug will be fixed in wyBuild 1.4 - out in about a week.
wyBuild fails
I was thinking about purchasing this tool but it appears that wyBuild fails while building patches for my program. Is there any sort of log produced anywhere when a patch build fails that I can send in?
Ok, the update is out - this should fix your problems.